There's a ton of information in the readme file that comes with the mod.

* When you see something like 575.0 (500.0), it means that the item is worth 575 with enchantments and the currently socketed gems, or 500 with no enchantments (and whatever value has been given to sockets).

* The red/green highlight in the compare window just shows which item has the higher value. The compare window always compares items without enchantments.